› 7vf3

X-ray diffraction
2.29Å resolution

Plexin B1 extracellular fragment in complex with lasso-grafted PB1m7 peptide

Released:
DOI: 10.2210/pdb7vf3/pdb
PDB entry 7vf3 coloured by chain, front view.
PDB entry 7vf3 coloured by chain, side view.
PDB entry 7vf3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
De novo Fc-based receptor dimerizers differentially modulate PlexinB1 function.
Sugano-Nakamura N, Matoba K, Hirose M, Bashiruddin NK, Matsunaga Y, Yamashita K, Hirata K, Yamamoto M, Arimori T, Suga H, Takagi J
Structure (2022)
PMID: 35981535

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128843 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Plexin-B1 Chains: A, C
Molecule details ›
Chains: A, C
Length: 525 amino acids
Theoretical weight: 56.66 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O43157 (Residues: 19-535; Coverage: 24%)
Gene names: KIAA0407, PLXN5, PLXNB1, SEP
Sequence domains:
Uteroglobin Chains: B, D
Molecule details ›
Chains: B, D
Length: 155 amino acids
Theoretical weight: 17.48 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P11684 (Residues: 21-19, 20-24, 25-91; Coverage: 97%)
Gene names: CC10, CCSP, SCGB1A1, UGB
Sequence domains: Uteroglobin family

Ligands and Environments

4 bound ligands:
Ligand NAG 2 x NAG
Ligand PEG 1 x PEG
Ligand PGE 1 x PGE
Ligand PG4 4 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: I4122
Unit cell:
a: 263.591Å b: 263.591Å c: 108.379Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.226
Expression system: Homo sapiens

Quick links

Citations

2 citation in other articles

Designing receptor agonists with enhanced pharmacokinetics by grafting macrocyclic peptides into fragment crystallizable regions.
Sakai et al. (2023)
1 more